Enterprise Architect by Sparx can generate sequence diagrams for you, but it means running the code inside the UML tool.
Just about every tool I know of can generate class diagrams for you, of varying fidelity, but sequence diagrams are another animal. You have to tell it where the flows start. I don't see how a tool will read your mind. Doubly so if there's a UI involved. You don't have every JSP in a web app represented as UML, do you? What if you're just using straight HTML pages and no JSPs?
Personally, I don't find sequence diagrams to be all that useful. They lose their value once they exceed a certain level of complexity, as do all diagrams.
UPDATE: If EA is too pricey for you, I'd recommend JUDE (now Astah). The community edition used to be quite good - it even did Java import and diagram generation. Now I see that it's been stripped of that capability. A professional license for Astah is still only $280.